Since the days of Darwin, the "tree of life" has been the preeminent metaphor for the process of evolution, reflecting the gradual branching and changing of individual species.

The discovery that a large cluster of genes appears to have jumped directly from one species of fungus to another, however, significantly strengthens the argument that a different metaphor, such as a mosaic, may be more appropriate.

Hundreds of years ago, when astronomers still held to a geocentric model of the solar system, they would often encounter data that ran directly counter to that model. Sometimes planets would appear to temporarily move backwards in what they called "retrograde motion." These early scientists explained away the bad data by inventing the "epicycle." Epicycles didn't actually explain anything; they were adopted for the purpose of saving the bad geocentric model of the solar system from falsification. Eventually, scientists accepted that planets weren't moving backwards and realized that the geocentric model of the solar system was simply wrong. Planets orbited the sun, not the earth.

Proponents of neo-Darwinian evolution have their modern day epicycles to attempt to explain why data often runs counter to the tree of life hypothesis. They have a mechanism to explain away the fact that a large cluster of similar genes appears in two groups where the common ancestor isn't thought to have had those genes. Their epicycle is called horizontal gene transfer (HGT), also known as lateral gene transfer (LGT). The article explains how the investigators invoke this common epicycle:

Rokas and Slot discovered that millions of years ago, a cluster of 23 genes jumped from one strain of mold commonly found on starchy foods like bread and potatoes, Aspergillus, to another strain of mold that lives in herbivore dung and specializes in breaking down plant fibers, Podospora.

The findings came as a major surprise, as there are only a handful of cases in recent evolutionary history where this type of gene transfer between organisms, known as horizontal gene transfer, has been reported in complex cells like those found in plants, animals and fungi.

Of course the problem is that in evolutionary biology, genomic data that doesn't fit with the standard tree is taken as evidence FOR horizontal gene transfer. As one article states: "topological discordance between a gene tree and a trusted reference tree is taken as a prima facie instance of LGT [lateral gene transfer]." (Mark A. Ragan and Robert G. Beiko, "Lateral genetic transfer: open issues," Philosophical Transactions of the Royal Society B, Vol. 364:2241-2251 (2009).) There appears to be no data that can falsify the tree of life: if the data doesn't fit with the tree, they just chock it up to the epicycle of horizontal gene transfer.

Thus when you hold the tree of life with an unscientific and unfalsifiable mindset, breakdowns in the tree of life become evidence for HGT. The article uses this very logic to infer HGT:

Since the 1980's, however, evolutionary scientists have become increasingly aware that horizontal or lateral gene transfer also plays a major role in evolution. In vertical gene transfer, all the genetic material in each new species come from a single ancestral species. In horizontal gene transfer, by contrast, species that receive bits of genetic material from its neighbors are directly related to a number of often unrelated species.

Horizontal gene transfer was first discovered in bacteria, and has been recognized as largely responsible for the problem of drug resistance. If one bacterium evolves a method for surviving a drug, this ability can spread rapidly to other unrelated microorganisms via horizontal gene transfer, substantially reducing the drug's effectiveness.

Though researchers now generally agree that horizontal gene transfer is relatively common among simple organisms like bacteria, they have continued to assume that it remained relatively rare among complex organisms like plants and animals.

"The thinking has been that there is very little horizontal gene transfer among plants and animals except for a few big, ancient events and maybe the occasional transfer of a single gene here or there," Slot said. "Our discovery suggests that the horizontal transfer of gene clusters may have been a big player not only in the evolution of bacteria but also in more complex organisms."

Is there any way to test universal common ancestry? There should be, and it seems the tree of life is not passing those tests. But if you simply invoke epicycles like "horizontal gene transfer" every time you get bad data, then you're not treating universal common ancestry like a falsifiable scientific hypothesis.